A new combined quantum mechanical (QM) and molecular mechanical (MM) technique is proposed. The method has an intuitive approach to partition total energy into QM and MM contributions. The number of electrons of QM region is controlled by a variable chemical potential and the requirement of a well-defined closed-shell QM region is no longer needed. The contribution of QM region is enhanced by a buffer region approach this approach circumvents the boundary problem in conventional combined QM/MM methods and the accuracy of QM results should be enhanced. This method is also proposed to apply to DNA molecular systems. We will focus on the effect of the methylation of DNA molecules. The application includes the calculations on structures and energies, and the simulation of the methylation process of DNA (Cytosine-5-)-methyltransferase. We hope this work will provide an accurate and efficient approach for biomolecular system.